Among the large number of illnesses caused by bacteria, perhaps the most common is diarrhea. According to the World Health Organization, of the millions of deaths each year worldwide from diarrheal disease, most are caused by contaminated food and water, poor hygiene, or improper sanitation practices. Pathogenic Escherichia coli (E. coli) accounts for the second largest cause of these infections. Even in the United States, where mechanisms and practices are well developed to prevent transmission; there were over thirty thousand hospitalizations and nine hundred deaths involving E. coli between 1982 and 2002. Beyond diarrhea, the common and preeminent virulent O157:H7 serotype can cause severe or even fatal damage to vascular, urinary and nephrology systems. While this provides a specific and poignant example, there are a myriad of other clinically significant pathogenic bacteria along with innumerable benign and beneficial ones. It is of utmost importance to quickly detect and accurately differentiate between serotypes to effect appropriate treatment of patients and minimize spread of dangerous strains.
In response to recent non-O157 outbreaks of toxigenic E. coli, in January 2011 the US congress passed the Food Safety Modernization Act, which mandates zero tolerance for a number of pathogenic bacteria, including E. coli serotypes O157, O26, O45, O103, O111, O121 and O145. Producers have been required to hold products for a week or more until cleared; this requirement has had a significant impact on the cost of food production. The CDC has identified improved surveillance of E. coli and development of tools for more rapid detection of emerging diarrheagenic E. coli strains as both challenges and opportunities. Yet these pathogenic strains must be detected within a microbial ecosystem containing huge numbers of Enterobacteriaceae.
There are standard laboratory methods for the detection, isolation and identification of pathogenic E. coli, where human capital is the constraining resource. Correct identification of pathogen-positive samples using serotyping requires extensive training. Conventional microbiological methods require approximately two days to perform primary enrichment, selective enrichment, and plating on different media for isolation of bacterial species and serotypes present in a sample. Additional characterization linking pathogen to contamination source requires serological bio-typing of cellular and flagellar antigens, requiring another 2-3 days. The addition of genotyping provides toxigenicity information based on plasmid toxin genes and requires approximately 3 days; this can be simultaneous with serology but requires resourcing of additional laboratory personnel. Genotyping by pulsed-field gel electrophoresis allows more refined comparison of strains on a global scale, but requires subjective individual judgment of banding patterns by an even more extensively trained certified analyst. In clinical situations, as this labor intensive and time consuming process is performed, the patient is being treated symptomatically or for a non-specific infection and the pathogenic strain continues to spread to other victims. For producers, any decrease in the time to determine E. coli O-side antigen would allow removal of contaminated food product from commerce more quickly, improving morbidity and mortality outcomes of humans and animals.